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scrime

Analysis of High-Dimensional Categorical Data Such as SNP Data

Tools for the analysis of high-dimensional data developed/implemented at the group "Statistical Complexity Reduction In Molecular Epidemiology" (SCRIME). Main focus is on SNP data. But most of the functions can also be applied to other types of categorical data.

Functions (38)

abf

Approximate Bayes Factor

analyse.models

Summarize MCMC sample of Bayesian logic regression models

buildSNPannotation

Construct Annotation for Affymetrix SNP Chips

colEpistatic

Cordell's Test for Epistatic Interactions

computeContCells

Pairwise Contingency Tables

computeContClass

Rowwise Contigency Tables

fblr

Full Bayesian Logic Regression for SNP Data

gknn

Generalized k Nearest Neighbors

identifyMonomorphism

Identification of Constant Variables

knncatimpute

Missing Value Imputation with kNN

knncatimputeLarge

Missing Value Imputation with kNN for High-Dimensional Data

pamCat

Prediction Analysis of Categorical Data

pcc

Pearson's Contingency Coefficient

predict.pamCat

Predict Method for pamCat Objects

predictFBLR

Predict Case Probabilities with Full Bayesian Logic Regression

recodeAffySNP

Recoding of Affymetrix SNP Values

recodeSNPs

Recoding of SNP Values

rowCATTs

Rowwise Cochran-Armitage Trend Test Based on Tables

rowChisq2Class

Rowwise Pearson's ChiSquare Test Based on Tables

rowChisqStats

Rowwise Pearson's ChiSquare Statistic

rowCors

Rowwise Correlation with a Vector

rowFreqs

Rowwise Frequencies

rowHWEs

Rowwise Test for Hardy-Weinberg Equilibrium

rowMAFs

Rowwise Minor Allele Frequency

rowMsquares

Rowwise Linear Trend Test Based on Tables

rowScales

Rowwise Scaling

rowTables

Rowwise Tables

rowTrendFuzzy

Trend Test for Fuzzy Genotype Calls

rowTrendStats

Rowwise Linear Trend Tests

scrime-internal

Internal scrime functions

shortenGeneDescription

Shorten the Gene Description

showChanges

Displaying Changes

simulateSNPcatResponse

Simulation of SNP Data with Categorical Response

simulateSNPglm

Simulation of SNP data

simulateSNPs

Simulation of SNP data

smc

Simple Matching Coefficient and Cohen's Kappa

snp2bin

Transformation of SNPs to Binary Variables

summary.simSNPglm

Summarizing a simSNPglm object

scrime

Analysis of High-Dimensional Categorical Data Such as SNP Data

v1.3.5
GPL-2
Authors
Holger Schwender, with a contribution of Arno Fritsch
Initial release
2018-12-01

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